The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie’s Stochastic Simulation Algorithm (SSA) is a standard algorithm to simulate well-stirred biochemical systems, butthe computational burden makes this algorithm slow to compute for many realistic problems. Recent programmability improvements allow […]

The performance and the level of programmability of graphics processors (GPU) on current video cards offer new capabilities beyond the graphics applications for which they were designed. These are general-purpose computations which expose parallelism. In this thesis, I describe the iterative methods for solving sparse linear systems: the Jacobi, Gauss-Seidel, Conjugate Gradient and BiConjugate Gradient […]

Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.